diff --git a/src/main/logseq/cli/config.cljs b/src/main/logseq/cli/config.cljs
index 90db4fb1b2..7b73207ac4 100644
--- a/src/main/logseq/cli/config.cljs
+++ b/src/main/logseq/cli/config.cljs
@@ -4,9 +4,9 @@
             [clojure.string :as string]
             [goog.object :as gobj]
             ["fs" :as fs]
-            ["os" :as os]
             ["path" :as node-path]
-            [logseq.cli.output-mode :as output-mode]))
+            [logseq.cli.output-mode :as output-mode]
+            [logseq.cli.root-dir :as root-dir]))
 
 (defn- parse-int
   [value]
@@ -30,19 +30,15 @@
 
     :else nil))
 
-(defn- default-root-dir
-  []
-  "~/logseq")
-
 (defn- default-config-path
   ([]
-   (default-config-path (default-root-dir)))
+   (default-config-path (root-dir/default-root-dir)))
   ([root-dir]
    (node-path/join root-dir "cli.edn")))
 
 (defn server-list-path
   [root-dir]
-  (node-path/join (or root-dir (node-path/join (.homedir os) "logseq")) "server-list"))
+  (node-path/join (or root-dir (root-dir/default-root-dir)) "server-list"))
 
 (def ^:private removed-config-keys
   #{:auth-token :retries :e2ee-password})
@@ -67,7 +63,7 @@
 
 (defn update-config!
   [{:keys [config-path root-dir]} updates]
-  (let [path (or config-path (default-config-path (or root-dir (default-root-dir))))
+  (let [path (or config-path (default-config-path (root-dir/normalize-root-dir root-dir)))
         current (or (read-config-file path) {})
         filtered-current (sanitize-file-config current)
         filtered-updates (sanitize-file-config updates)
@@ -115,21 +111,23 @@
                   :logout-timeout-ms 120000
                   :list-title-max-display-width list-title-max-display-width-default
                   :output-format nil
-                  :root-dir (default-root-dir)
+                  :root-dir (root-dir/default-root-dir)
                   :ws-url "wss://api.logseq.io/sync/%s"
                   :http-base "https://api.logseq.io"}
         env (env-config)
-        root-dir (or (:root-dir opts)
-                     (:root-dir env)
-                     (:root-dir defaults))
+        root-dir (root-dir/normalize-root-dir
+                  (or (:root-dir opts)
+                      (:root-dir env)
+                      (:root-dir defaults)))
         config-path (or (:config-path opts)
                         (:config-path env)
                         (default-config-path root-dir))
         file-config (or (read-config-file config-path) {})
-        root-dir (or (:root-dir opts)
-                     (:root-dir env)
-                     (:root-dir file-config)
-                     root-dir)
+        root-dir (root-dir/normalize-root-dir
+                  (or (:root-dir opts)
+                      (:root-dir env)
+                      (:root-dir file-config)
+                      root-dir))
         output-format (or (output-mode/parse (:output-format opts))
                           (output-mode/parse (:output opts))
                           (output-mode/parse (:output-format env))
diff --git a/src/test/logseq/cli/config_test.cljs b/src/test/logseq/cli/config_test.cljs
index ace5c1a0e5..c2a9c78590 100644
--- a/src/test/logseq/cli/config_test.cljs
+++ b/src/test/logseq/cli/config_test.cljs
@@ -48,7 +48,7 @@
         result (with-env env #(config/resolve-config opts))]
     (is (= cfg-path (:config-path result)))
     (is (= "cli-repo" (:graph result)))
-    (is (= "cli-root" (:root-dir result)))
+    (is (= (node-path/resolve "cli-root") (:root-dir result)))
     (is (= 333 (:timeout-ms result)))
     (is (= 888 (:login-timeout-ms result)))
     (is (= 999 (:logout-timeout-ms result)))
@@ -65,7 +65,7 @@
              "LOGSEQ_CLI_ROOT_DIR" "env-root"}
         result (with-env env #(config/resolve-config {:config-path cfg-path}))]
     (is (= "env-repo" (:graph result)))
-    (is (= "env-root" (:root-dir result)))))
+    (is (= (node-path/resolve "env-root") (:root-dir result)))))
 
 (deftest test-output-format-env-overrides-file
   (let [dir (node-helper/create-tmp-dir)
@@ -110,7 +110,7 @@
                           "LOGSEQ_CLI_CONFIG" nil}
                  #(config/resolve-config {:config-path cfg-path}))]
     (is (= cfg-path (:config-path result)))
-    (is (= "~/logseq" (:root-dir result)))
+    (is (= (node-path/join (.homedir os) "logseq") (:root-dir result)))
     (is (= "wss://api.logseq.io/sync/%s" (:ws-url result)))
     (is (= "https://api.logseq.io" (:http-base result)))
     (is (= 10000 (:timeout-ms result)))
@@ -127,8 +127,8 @@
                           "LOGSEQ_CLI_OUTPUT" nil
                           "LOGSEQ_CLI_CONFIG" nil}
                  #(config/resolve-config {:root-dir "~/custom-logseq"}))]
-    (is (= "~/custom-logseq" (:root-dir result)))
-    (is (= (node-path/join "~/custom-logseq" "cli.edn")
+    (is (= (node-path/join (.homedir os) "custom-logseq") (:root-dir result)))
+    (is (= (node-path/join (.homedir os) "custom-logseq" "cli.edn")
            (:config-path result)))))
 
 (deftest test-explicit-config-path-does-not-change-root-dir-derived-defaults
@@ -137,7 +137,7 @@
         result (config/resolve-config {:config-path cfg-path
                                        :root-dir "~/custom-logseq"})]
     (is (= cfg-path (:config-path result)))
-    (is (= "~/custom-logseq" (:root-dir result)))))
+    (is (= (node-path/join (.homedir os) "custom-logseq") (:root-dir result)))))
 
 (deftest test-server-list-path-follows-root-dir
   (let [root-dir (node-path/join (node-helper/create-tmp-dir "cli-root") "nested-root")
@@ -202,3 +202,11 @@
         parsed (reader/read-string contents)]
     (is (= "old" (:graph parsed)))
     (is (not (contains? parsed :auth-token)))))
+
+(deftest test-update-config-expands-tilde-in-root-dir
+  (let [dir (node-helper/create-tmp-dir "cli-tilde")
+        cfg-path (node-path/join dir "cli.edn")
+        _ (config/update-config! {:root-dir dir} {:ws-url "wss://example.com"})
+        contents (.toString (fs/readFileSync cfg-path) "utf8")
+        parsed (reader/read-string contents)]
+    (is (= "wss://example.com" (:ws-url parsed)))))